Ryan-
I had the same problem running 2" TTI's along with a TKO 600. My trans was not modified as heavy in the rear part as the newer tko's are. I cut out another 1/2" to clear the cross member and fabricated a new cover. I think this is how Keisler modifies them now too, reguarding their web site. This made room to raise the trans higher than where the flat top of a 4-speed hump go and brought the TTI's up where they belong. Pinion angle with stock rear springs came out correct.
My 68 Charger is an auto and I had to cut quite a lot out of the tunnel to get the trans in the right position. Dayclona is right. If you want a tko you need to cut the tunnel to line up everything. No way I was going to run the car with the headers pointing at the ground like they did in the first place!
After cutting the floor and raising the trans I testfitted a new AMD 4-speed hump with the intention of making it look look like a factory 4-speed, but, as mentioned, the top of the hump came in about 1/4" lower than the top of the shifter base plate. Solution was to make my own patch, put on carpet and console and go! My car sits at about stock hight, maybe a tad lower, and with 28" wheels I have about 5" distance from header flanges to ground and I no longer worry about bad roads.
I run a Lakewoos shattershield and did not have to grind it to fit the TTI's, but one nut on the bell flange had to be grinded a little and held in position when tightening the bolt.